def _verify_inputs(self):
user_lobsterin = Lobsterin.from_file(os.path.join(os.getcwd(), "lobsterin"))
# Check lobsterin
if self.get("check_lobsterin", True):
ref_lobsterin = Lobsterin.from_file(
os.path.join(self["ref_dir"], "inputs", "lobsterin")
)
params_to_check = self.get("params_to_check", [])
for p in params_to_check:
if user_lobsterin.get(p, None) != ref_lobsterin.get(p, None):
raise ValueError("lobsterin value of {} is inconsistent!".format(p))
logger.info("RunLobsterFake: verified inputs successfully")
def setUpClass(cls):
cls.ref_lobsterin = Lobsterin.from_file(
os.path.join(
module_dir,
"./../../test_files",
"lobster",
"Lobsterinputs",
"lobsterin",
))
cls.ref_lobsterin2 = Lobsterin.from_file(
os.path.join(module_dir, "./../../test_files", "lobster",
"lobsterins", "lobsterin2"))
cls.vasp_dir = os.path.join(module_dir, "./../../test_files",
"lobster", "VASP_calc_for_Lobster")
def test_ioset_explicit(self):
for fn in ["POSCAR.gz", "POTCAR.gz", "INCAR.gz"]:
shutil.copy2(os.path.join(self.vasp_dir, fn), ".")
ft = WriteLobsterinputfromIO(
poscar_path="POSCAR.gz",
potcar_path="POTCAR.gz",
incar_path="INCAR.gz",
option="standard",
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self.assertEqual(Lobsterin.from_file("lobsterin"), self.ref_lobsterin)
def test_ioset_settings(self):
for fn in ["POSCAR.gz", "POTCAR.gz", "INCAR.gz"]:
shutil.copy2(os.path.join(self.vasp_dir, fn), ".")
# user supplied lobsterin inputs
ft = WriteLobsterinputfromIO(
poscar_path="POSCAR.gz",
potcar_path="POTCAR.gz",
incar_path="INCAR.gz",
option="standard",
user_lobsterin_settings={"COHPEndEnergy": 10.0},
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self.assertEqual(Lobsterin.from_file("lobsterin"), self.ref_lobsterin2)
def run_task(self, fw_spec):
vasp_calc_dir = self.get("calc_dir", None)
vasp_calc_loc = (
get_calc_loc(self["calc_loc"], fw_spec["calc_locs"])
if self.get("calc_loc")
else {}
)
# get the directory that contains the Lobster dir to parse
current_dir = os.getcwd()
# parse the Lobster directory
logger.info("PARSING DIRECTORY: {}".format(current_dir))
task_doc = {}
struct = Structure.from_file(self._find_gz_file("POSCAR"))
Lobsterout_here = Lobsterout(self._find_gz_file("lobsterout"))
task_doc["output"] = Lobsterout_here.get_doc()
Lobsterin_here = Lobsterin.from_file(self._find_gz_file("lobsterin"))
task_doc["input"] = Lobsterin_here
try:
Lobsterin_orig = Lobsterin.from_file(self._find_gz_file("lobsterin.orig"))
task_doc["orig_input"] = Lobsterin_orig
except ValueError:
pass
# save custodian details
if os.path.exists("custodian.json"):
task_doc["custodian"] = loadfn("custodian.json")
additional_fields = self.get("additional_fields", {})
if additional_fields:
task_doc.update(additional_fields)
task_doc.update(get_meta_from_structure(struct))
if vasp_calc_dir != None:
task_doc["vasp_dir_name"] = vasp_calc_dir
else:
task_doc["vasp_dir_name"] = vasp_calc_loc["path"]
task_doc["dir_name"] = current_dir
# Check for additional keys to set based on the fw_spec
if self.get("fw_spec_field"):
task_doc.update(fw_spec[self.get("fw_spec_field")])
task_doc["state"] = "successful"
task_doc = jsanitize(task_doc)
# get the database connection
db_file = env_chk(self.get("db_file"), fw_spec)
# db insertion or taskdoc dump
if not db_file:
with open("task_lobster.json", "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
db = VaspCalcDb.from_db_file(db_file, admin=True)
db.collection = db.db["lobster"]
additional_outputs = self.get("additional_outputs", None)
if additional_outputs:
for filename in additional_outputs:
fs_id = None
if os.path.isfile(filename):
fs_id = put_file_in_gridfs(
filename, db, collection_name="lobster_files", compress=True
)
elif os.path.isfile(filename + ".gz"):
fs_id = put_file_in_gridfs(
filename + ".gz",
db,
collection_name="lobster_files",
compress=False,
compression_type="zlib",
)
if fs_id:
key_name = filename.split(".")[0].lower() + "_id"
task_doc[key_name] = fs_id
db.insert(task_doc)
return FWAction()